ClinVar Miner

Submissions for variant NM_006019.4(TCIRG1):c.303_309del (p.Glu102fs)

dbSNP: rs886048594
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000672867 SCV000373698 uncertain significance Autosomal recessive osteopetrosis 1 2017-04-27 criteria provided, single submitter clinical testing The TCIRG1 c.303_309delGGAGCGC (p.Glu102TrpfsTer62) variant results in a frameshift, and is predicted to result in premature termination of the protein. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. This variant is not found in the 1000 Genomes Project, the Exome Sequencing Project, or the Exome Aggregation Consortium. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of frameshift variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for osteopetrosis. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Counsyl RCV000672867 SCV000798015 likely pathogenic Autosomal recessive osteopetrosis 1 2018-02-20 criteria provided, single submitter clinical testing
Invitae RCV001850622 SCV002243163 pathogenic not provided 2021-03-17 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with TCIRG1-related conditions. ClinVar contains an entry for this variant (Variation ID: 305784). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change creates a premature translational stop signal (p.Glu102Trpfs*62) in the TCIRG1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TCIRG1 are known to be pathogenic (PMID: 10888887, 10942435, 11532986, 19448635).

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